"human"[ORGN] and PGK1 - SNP

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Select item 20070391.

rs2007039 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: X:78118027 (GRCh38)
X:77373524 (GRCh37)
Canonical SPDI:: NC_000023.11:78118026:C:T
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.226385/12477 (ALFA)
T=0.15/6 (GENOME_DK)
C=0.186916/40 (SGDP_PRJ)
T=0.196629/105 (MGP)
T=0.199031/575 (ALSPAC)
C=0.2/2 (Siberian)
T=0.203344/754 (TWINSUK)
T=0.266149/2810 (GoESP)
T=0.269803/27766 (GnomAD)
T=0.271366/49667 (GnomAD_exomes)
T=0.272736/23905 (ExAC)
T=0.287699/76151 (TOPMED)
T=0.333333/36 (Qatari)
T=0.344017/1299 (1000Genomes)
T=0.357679/1048 (KOREAN)
T=0.453404/5823 (TOMMO)
T=0.482993/71 (Vietnamese)
HGVS:: NC_000023.11:g.78118027C>T, NC_000023.10:g.77373524C>T, NG_008862.1:g.18859C>T, NW_003871101.3:g.675289C>T

Select item 20731762.

rs2073176 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: X:78122769 (GRCh38)
X:77378266 (GRCh37)
Canonical SPDI:: NC_000023.11:78122768:T:G
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.224578/16277 (ALFA)
G=0.15/6 (GENOME_DK)
T=0.186364/41 (SGDP_PRJ)
G=0.198502/106 (MGP)
G=0.198685/574 (ALSPAC)
G=0.203074/753 (TWINSUK)
T=0.25/2 (Siberian)
G=0.25/6 (PRJEB36033)
G=0.271331/27889 (GnomAD)
G=0.289962/76750 (TOPMED)
G=0.346722/1309 (1000Genomes)
G=0.351852/38 (Qatari)
G=0.358703/1051 (KOREAN)
G=0.358844/633 (HapMap)
G=0.453314/5822 (TOMMO)
T=0.456522/21 (Vietnamese)
HGVS:: NC_000023.11:g.78122769T>G, NC_000023.10:g.77378266T>G, NG_008862.1:g.23601T>G, NW_003871101.3:g.680031T>G

Select item 20731773.

rs2073177 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: X:78125505 (GRCh38)
X:77381002 (GRCh37)
Canonical SPDI:: NC_000023.11:78125504:A:G
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.251318/4673 (ALFA)
G=0.15/6 (GENOME_DK)
A=0.186916/40 (SGDP_PRJ)
G=0.196629/105 (MGP)
G=0.198339/573 (ALSPAC)
A=0.2/2 (Siberian)
G=0.201996/749 (TWINSUK)
G=0.268569/27405 (GnomAD)
G=0.286758/75902 (TOPMED)
G=0.333333/36 (Qatari)
G=0.3436/1297 (1000Genomes)
G=0.357582/1047 (KOREAN)
G=0.453425/5823 (TOMMO)
HGVS:: NC_000023.11:g.78125505A>G, NC_000023.10:g.77381002A>G, NG_008862.1:g.26337A>G, NW_003871101.3:g.682767A>G

Select item 20731784.

rs2073178 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,T [Show Flanks]
Chromosome:: X:78125517 (GRCh38)
X:77381014 (GRCh37)
Canonical SPDI:: NC_000023.11:78125516:G:A,NC_000023.11:78125516:G:T
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.16121/4948 (ALFA)
A=0.15/6 (GENOME_DK)
G=0.18692/40 (SGDP_PRJ)
A=0.19663/105 (MGP)
A=0.19799/572 (ALSPAC)
G=0.2/2 (Siberian)
A=0.20173/748 (TWINSUK)
A=0.33333/36 (Qatari)
A=0.34339/1296 (1000Genomes)
A=0.35748/1046 (KOREAN)
A=0.35911/627 (HapMap)
A=0.45333/5822 (TOMMO)
HGVS:: NC_000023.11:g.78125517G>A, NC_000023.11:g.78125517G>T, NC_000023.10:g.77381014G>A, NC_000023.10:g.77381014G>T, NG_008862.1:g.26349G>A, NG_008862.1:g.26349G>T, NW_003871101.3:g.682779G>A, NW_003871101.3:g.682779G>T

Select item 20766285.

rs2076628 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: X:78103825 (GRCh38)
X:77359322 (GRCh37)
Canonical SPDI:: NC_000023.11:78103824:G:A,NC_000023.11:78103824:G:C
Gene:: PGK1 (Varview)
Functional Consequence:: upstream_transcript_variant,2KB_upstream_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.07835/1077 (ALFA)
A=0.15/6 (GENOME_DK)
G=0.17857/35 (SGDP_PRJ)
A=0.20249/585 (ALSPAC)
A=0.20361/755 (TWINSUK)
G=0.21429/3 (Siberian)
A=0.25736/752 (KOREAN)
A=0.32219/4138 (TOMMO)
A=0.32609/1231 (1000Genomes)
A=0.36111/39 (Qatari)
A=0.48936/23 (Vietnamese)
HGVS:: NC_000023.11:g.78103825G>A, NC_000023.11:g.78103825G>C, NC_000023.10:g.77359322G>A, NC_000023.10:g.77359322G>C, NG_008862.1:g.4657G>A, NG_008862.1:g.4657G>C, NW_003871101.3:g.661087G>A, NW_003871101.3:g.661087G>C

PubMed

Select item 20766306.

rs2076630 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: X:78117733 (GRCh38)
X:77373230 (GRCh37)
Canonical SPDI:: NC_000023.11:78117732:A:G
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.228986/10559 (ALFA)
G=0.15/6 (GENOME_DK)
A=0.186916/40 (SGDP_PRJ)
G=0.199031/575 (ALSPAC)
A=0.2/2 (Siberian)
G=0.203614/755 (TWINSUK)
G=0.27145/28224 (GnomAD)
G=0.288137/76267 (TOPMED)
G=0.333333/36 (Qatari)
G=0.345057/1303 (1000Genomes)
G=0.357582/1047 (KOREAN)
G=0.453404/5823 (TOMMO)
A=0.479167/23 (Vietnamese)
HGVS:: NC_000023.11:g.78117733A>G, NC_000023.10:g.77373230A>G, NG_008862.1:g.18565A>G, NW_003871101.3:g.674995A>G

Select item 126881347.

rs12688134 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: X:78123613 (GRCh38)
X:77379110 (GRCh37)
Canonical SPDI:: NC_000023.11:78123612:T:G
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.245532/4424 (ALFA)
G=0.194185/561 (ALSPAC)
G=0.195523/725 (TWINSUK)
G=0.234978/21766 (GnomAD)
G=0.272696/799 (KOREAN)
G=0.277778/30 (Qatari)
G=0.284129/75206 (TOPMED)
G=0.33298/1257 (1000Genomes)
T=0.350467/75 (SGDP_PRJ)
G=0.442372/5650 (TOMMO)
T=0.5/2 (Siberian)
HGVS:: NC_000023.11:g.78123613T>G, NC_000023.10:g.77379110T>G, NG_008862.1:g.24445T>G, NW_003871101.3:g.680875T>G

Select item 171395888.

rs17139588 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: X:78104228 (GRCh38)
X:77359725 (GRCh37)
Canonical SPDI:: NC_000023.11:78104227:C:T
Gene:: PGK1 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.047734/889 (ALFA)
T=0.018519/2 (Qatari)
T=0.035059/3655 (GnomAD)
T=0.036564/9678 (TOPMED)
T=0.046202/174 (1000Genomes)
T=0.046926/174 (TWINSUK)
T=0.047421/137 (ALSPAC)
T=0.05/2 (GENOME_DK)
T=0.08897/1142 (TOMMO)
T=0.120288/351 (KOREAN)
C=0.184211/7 (SGDP_PRJ)
C=0.25/1 (Siberian)
HGVS:: NC_000023.11:g.78104228C>T, NC_000023.10:g.77359725C>T, NG_008862.1:g.5060C>T, NM_000291.3:c.-113C>T, NW_003871101.3:g.661490C>T

Select item 173034139.

rs17303413 [Homo sapiens]

Variant type:: SNV
Alleles:: G>C [Show Flanks]
Chromosome:: X:78124810 (GRCh38)
X:77380307 (GRCh37)
Canonical SPDI:: NC_000023.11:78124809:G:C
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.159449/2953 (ALFA)
C=0.091155/344 (1000Genomes)
C=0.1/4 (GENOME_DK)
C=0.130738/13514 (GnomAD)
C=0.133405/35311 (TOPMED)
C=0.136704/73 (MGP)
C=0.164509/610 (TWINSUK)
C=0.164763/476 (ALSPAC)
G=0.166667/1 (Siberian)
C=0.175926/19 (Qatari)
G=0.2125/17 (SGDP_PRJ)
HGVS:: NC_000023.11:g.78124810G>C, NC_000023.10:g.77380307G>C, NG_008862.1:g.25642G>C, NW_003871101.3:g.682072G>C

Select item 7816504110.

rs78165041 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,T [Show Flanks]
Chromosome:: X:78113798 (GRCh38)
X:77369295 (GRCh37)
Canonical SPDI:: NC_000023.11:78113797:G:A,NC_000023.11:78113797:G:T
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000868/20 (ALFA)
A=0.000426/78 (GnomAD_exomes)
A=0.00054/46 (ExAC)
A=0.001446/150 (GnomAD)
A=0.001519/402 (TOPMED)
A=0.002083/22 (GoESP)
A=0.004579/17 (1000Genomes)
HGVS:: NC_000023.11:g.78113798G>A, NC_000023.11:g.78113798G>T, NC_000023.10:g.77369295G>A, NC_000023.10:g.77369295G>T, NG_008862.1:g.14630G>A, NG_008862.1:g.14630G>T, NM_000291.4:c.171G>A, NM_000291.4:c.171G>T, NM_000291.3:c.171G>A, NM_000291.3:c.171G>T, NW_003871101.3:g.671060G>A, NW_003871101.3:g.671060G>T

Select item 11311227311.

rs113112273 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: X:78124580 (GRCh38)
X:77380077 (GRCh37)
Canonical SPDI:: NC_000023.11:78124579:A:G
Gene:: PGK1 (Varview)
Functional Consequence:: intron_variant
Clinical significance:: benign
Validated:: by frequency,by alfa,by cluster
MAF:: G=0.232364/8103 (ALFA)
G=0.15/6 (GENOME_DK)
A=0.186916/40 (SGDP_PRJ)
G=0.198685/574 (ALSPAC)
G=0.203344/754 (TWINSUK)
A=0.25/2 (Siberian)
G=0.268763/27620 (GnomAD)
G=0.287415/76076 (TOPMED)
G=0.333333/36 (Qatari)
G=0.344017/1299 (1000Genomes)
G=0.358362/1050 (KOREAN)
G=0.453404/5823 (TOMMO)
A=0.458333/22 (Vietnamese)
HGVS:: NC_000023.11:g.78124580A>G, NC_000023.10:g.77380077A>G, NG_008862.1:g.25412A>G, NW_003871101.3:g.681842A>G

Select item 13785252812.

rs137852528 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: X:78123240 (GRCh38)
X:77378737 (GRCh37)
Canonical SPDI:: NC_000023.11:78123239:G:A
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: pathogenic
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
HGVS:: NC_000023.11:g.78123240G>A, NC_000023.10:g.77378737G>A, NG_008862.1:g.24072G>A, NM_000291.4:c.802G>A, NM_000291.3:c.802G>A, NW_003871101.3:g.680502G>A, NP_000282.1:p.Asp268Asn

Select item 13785252913.

rs137852529 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: X:78118146 (GRCh38)
X:77373643 (GRCh37)
Canonical SPDI:: NC_000023.11:78118145:G:A,NC_000023.11:78118145:G:C
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: pathogenic
Validated:: by frequency,by alfa,by cluster
MAF:: A=0.000111/1 (ALFA)
A=0.000011/2 (GnomAD_exomes)
HGVS:: NC_000023.11:g.78118146G>A, NC_000023.11:g.78118146G>C, NC_000023.10:g.77373643G>A, NC_000023.10:g.77373643G>C, NG_008862.1:g.18978G>A, NG_008862.1:g.18978G>C, NM_000291.4:c.617G>A, NM_000291.4:c.617G>C, NM_000291.3:c.617G>A, NM_000291.3:c.617G>C, NW_003871101.3:g.675408G>A, NW_003871101.3:g.675408G>C, NP_000282.1:p.Arg206Gln, NP_000282.1:p.Arg206Pro

LitVar

Select item 13785253014.

rs137852530 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: X:78124992 (GRCh38)
X:77380489 (GRCh37)
Canonical SPDI:: NC_000023.11:78124991:C:A
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: other
HGVS:: NC_000023.11:g.78124992C>A, NC_000023.10:g.77380489C>A, NG_008862.1:g.25824C>A, NM_000291.4:c.1055C>A, NM_000291.3:c.1055C>A, NW_003871101.3:g.682254C>A, NP_000282.1:p.Thr352Asn

Select item 13785253115.

rs137852531 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: X:78113890 (GRCh38)
X:77369387 (GRCh37)
Canonical SPDI:: NC_000023.11:78113889:T:C
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: pathogenic
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.002/1 (ALFA)
HGVS:: NC_000023.11:g.78113890T>C, NC_000023.10:g.77369387T>C, NG_008862.1:g.14722T>C, NM_000291.4:c.263T>C, NM_000291.3:c.263T>C, NW_003871101.3:g.671152T>C, NP_000282.1:p.Leu88Pro

Select item 13785253216.

rs137852532 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: X:78117367 (GRCh38)
X:77372864 (GRCh37)
Canonical SPDI:: NC_000023.11:78117366:G:T
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: pathogenic
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
HGVS:: NC_000023.11:g.78117367G>T, NC_000023.10:g.77372864G>T, NG_008862.1:g.18199G>T, NM_000291.4:c.473G>T, NM_000291.3:c.473G>T, NW_003871101.3:g.674629G>T, NP_000282.1:p.Gly158Val

LitVar

Select item 13785253317.

rs137852533 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: X:78124883 (GRCh38)
X:77380380 (GRCh37)
Canonical SPDI:: NC_000023.11:78124882:T:C
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: pathogenic
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.002/1 (ALFA)
HGVS:: NC_000023.11:g.78124883T>C, NC_000023.10:g.77380380T>C, NG_008862.1:g.25715T>C, NM_000291.4:c.946T>C, NM_000291.3:c.946T>C, NW_003871101.3:g.682145T>C, NP_000282.1:p.Cys316Arg

LitVar

Select item 13785253418.

rs137852534 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: X:78123196 (GRCh38)
X:77378693 (GRCh37)
Canonical SPDI:: NC_000023.11:78123195:T:C
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: uncertain-significance
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.000206/3 (ALFA)
C=0.000008/2 (TOPMED)
C=0.000011/2 (GnomAD_exomes)
C=0.000045/1 (TOMMO)
HGVS:: NC_000023.11:g.78123196T>C, NC_000023.10:g.77378693T>C, NG_008862.1:g.24028T>C, NM_000291.4:c.758T>C, NM_000291.3:c.758T>C, NW_003871101.3:g.680458T>C, NP_000282.1:p.Ile253Thr

Select item 13785253519.

rs137852535 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: X:78123292 (GRCh38)
X:77378789 (GRCh37)
Canonical SPDI:: NC_000023.11:78123291:A:T
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: pathogenic
Validated:: by cluster
HGVS:: NC_000023.11:g.78123292A>T, NC_000023.10:g.77378789A>T, NG_008862.1:g.24124A>T, NM_000291.4:c.854A>T, NM_000291.3:c.854A>T, NW_003871101.3:g.680554A>T, NP_000282.1:p.Asp285Val

LitVar

Select item 13785253620.

rs137852536 [Homo sapiens]

Variant type:: SNV
Alleles:: T>A [Show Flanks]
Chromosome:: X:78113767 (GRCh38)
X:77369264 (GRCh37)
Canonical SPDI:: NC_000023.11:78113766:T:A
Gene:: PGK1 (Varview)
Functional Consequence:: coding_sequence_variant,missense_variant
Clinical significance:: pathogenic
Validated:: by cluster
HGVS:: NC_000023.11:g.78113767T>A, NC_000023.10:g.77369264T>A, NG_008862.1:g.14599T>A, NM_000291.4:c.140T>A, NM_000291.3:c.140T>A, NW_003871101.3:g.671029T>A, NP_000282.1:p.Ile47Asn

LitVar

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